[Freesurfer] Queries about semi-inflated surface for overlay

Dear Freesurfer experts, I would like to overlay the significance map and gamma.mgh map from cortical thickness GLM on a semi-inflated surface according to one previous post in the mailing list (shown as below) by using the command (shown) under the directory of fsaverage. https://mail.nmr.mgh

Re: [Freesurfer] asegstats2table Longitudinal data.

Thanks Martin, The provided command works! Best, Victor Hospital de Sant Pau, Barcelona ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

Hi, Ok, thank you! One additional follow up: Once I converted the lh.white (freesurfer) to the lh.white.gii (gifti), the converted surface (.gii) does not fit on the structural scan from freesurfer anymore (neither brain.mgz or orig.mgz or nu.omz). How can I register my freesurfer structural da

[Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at 434

Dear Experts, during an fsfast analysis an error occured after selxavg3-sess was executed. The corresponding commands were: mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 -analysis analy

[Freesurfer] tumor mask

Dear Freesurfers, I would like to run recon-all on patients with brain tumors. Can I add a previously created tumor mask along with the mprage to improve the segmentation? If so, how to do it? Thank you! Andrea -- *Andrea Horváth M.D.* PhD Fellow Diagnostic Centre of Pécs horvath.andr...@pte.h

Re: [Freesurfer] Queries about semi-inflated surface for overlay

1. Doing it on fsaverage is fine. 2. You can run mris_inflate -w 1 -scale 1 lh.white lh.inflated and it will generate a snapshot every step of the integration so you can pick which one you want. cheers Bruce On Mon, 2 Jun 2014, Zixuan Yang wrote: Dear Freesurfer experts,   I would like

Re: [Freesurfer] CUDA problem with FreeSurfer 5.3.0 on CentOS6

Bump. Having the same problem with a similar setup. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is ad

[Freesurfer] software for registering two flatmaps

Hello, Can the Freesurfer software register two flatmaps that are not created in Freesurfer? Would they just need to be converted? And which program is appropriate? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in C

Re: [Freesurfer] software for registering two flatmaps

no, we don't register flat maps. You'll need the MRI data cheers Bruce On Mon, 2 Jun 2014, Anthony Dick wrote: > Hello, > > Can the Freesurfer software register two flatmaps that are not created > in Freesurfer? Would they just need to be converted? And which program > is appropriate? > > Anthony

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

Bastian, Are you using freeview to display the surface? If so, you will need to get the newest freeview.bin, which is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/ this has been updated to read the new volume geometry info now included in the lh.white

[Freesurfer] freesurfer v5.3 TRACULA longitudinnal error

Hi Anastasia I switched from FS v.5.2 to v.5.3 and I am still having this error when running TRACULA longitudinal freesurfer stream despite running with freesurfer v5.3 (both recon-all and trac-all). I am sending along the dmrirc file and the log file. Could you check what may be causing this p

[Freesurfer] TRACULA: ERROR in -qa Flag

Dear Anastasia and Freesurfer experts, I am trying to set up an analysis of motion parameters using the flag -q from a set of DTI Dicoms located on the Martinos cluster, but I am facing problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to Freesurfer5.3 and FSL. What am I doing

Re: [Freesurfer] Longitudinal design

HI Tudor, you can run the -long processes in parallel. Something else is wrong. Check if you have enough disk space. Re-run the long from scratch (to make sure everything is generated new). Best, Martin On Jun 2, 2014, at 5:34 PM, Tudor Popescu wrote: > Hi Bruce > > I suspected this might b